WASHINGTON — Defense Secretary Chuck Hagel acknowledged Wednesday that there were “a lot of red flags” in the past of alleged Washington Navy Yard shooter Aaron Alexis, and he ordered top-to-bottom reviews of background checks for security clearances and procedures for gaining access to U.S. military facilities worldwide.

Alexis’ mother said she had no answers for why her son allegedly opened fire Monday morning and killed 12 people at the Navy Yard before he was slain by police.

“I don’t know why he did what he did, and I’m not going to be able to ask him why,” Cathleen Alexis told reporters. “Aaron is now in a place where he can no longer do harm to anyone, and for that I am glad. To families of the victims, I am so, so very sorry that this has happened. My heart is broken.”

Countering earlier reports that Alexis, 34, had been treated for mental health problems, the Department of Veterans Affairs said he sought no such treatment after enrolling in the military’s health care system in February 2011. That was several months before Alexis received an honorable discharge from the Navy after serving four years as a reservist. Alexis could have seen mental health counselors outside the VA hospital and clinic system before or after enrolling in it.

Alexis did visit the emergency room at the VA Medical Center in Providence, R.I., four weeks ago, complaining of insomnia. He received sleeping pills, with instructions to have a follow-up exam by a doctor, the VA said. He went to the VA Medica Center in Washington, D.C., five days later, on Aug. 28, blamed his insomnia on his work schedule, and received a refill, according to the VA.

Alexis’ visit to the Rhode Island hospital on Aug. 23 came 16 days after police in Newport, R.I., visited him at a Marriott hotel about his complaints that three people had followed him from Virginia “to keep him awake by talking to him and sending vibrations into his body,” according to a police report.

Since last December, Alexis had been receiving military disability benefits of $395 a month for orthopedic problems and tinnitus, or ringing in the ears, the VA said.

From 2004 to 2010, before and during his Navy service, Alexis was arrested three times in three states, twice for suspicious gun discharges. Yet he received a “Secret” security clearance in 2008 that was not revoked as he left the Navy and later took a job as a computer technician at the Navy Yard for The Experts, a Fort Lauderdale, Fla.-based federal subcontractor.

“Obviously, there were a lot of red flags,” Hagel said at a Pentagon news briefing. “Why they didn’t get picked (up), why they didn’t get incorporated into the clearance process, what he was doing; those are all legitimate questions that we’re going to be dealing with. How do we fix it?”

Sen. Claire McCaskill, a Missouri Democrat who chairs a Senate subcommittee on federal contractors, expressed concern that Alexis’ security clearance was good for 10 years and remained in effect, despite his run-ins with police and signs of mental problems.

“One of the things that’s most troubling about this is there would have been police involvement with a military contractor who was hallucinating, and we don’t have a mechanism for that information to be quickly and effectively communicated in a way that that clearance is removed,” she said Wednesday in a call with reporters.

McCaskill, along with Democratic Sen. Jon Tester of Montana and Republican Sens. Rob Portman of Ohio and Ron Johnson of Wisconsin, wrote a letter Wednesday to Patrick McFarland, inspector general of the Office of Personnel Management, asking who had performed Alexis’ security screenings, when they were done and whether they’d given proper scrutiny to his “pattern of misconduct.”

The agency said in a statement issued late Tuesday that it “had conducted the background security clearance investigation for Aaron Alexis in 2007” that led to him receiving the “Secret” clearance the next year.

The OPM check revealed Alexis’ 2004 arrest in Seattle for shooting out the tires of construction workers' car parked near his home, Thomas Richards, a spokesman for OPM, said Wednesday.

In addition to his police encounters, Alexis had multiple disciplinary problems as a Navy reservist, according to the Pentagon.

Hagel said his wide-ranging probe would include an examination of why the Newport, R.I., police report to the Navy about Alexis’ strange behavior did not impact his security clearance or his ability to access the Navy Yard.

The Navy Yard had been cited for security lapses before the shooting rampage. Appearing alongside Hagel, Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, said security there had not been degraded by budget cuts that Congress has imposed on the Pentagon.

Dempsey said he still supports the Pentagon’s decision of several years ago to remove questions about mental health from application forms for security clearances in order to “de-stigmatize” veterans suffering from post-traumatic stress disorder, which in many cases has been tied to their service in Iraq or Afghanistan.

Dempsey said “men and women should have the opportunity to overcome their mental disorders or their mental challenges or their clinical health challenges and shouldn’t be stigmatized.”

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